We studied for first time the seasonal variations of planktic foraminifera off Iquique (20°S, 70°W) and Concepcion (36°S, 74°W), Chile. The samples were collected by sediment traps located at two depths: 1000 and 2300 m between September and December 2005, under normal conditions (with permanent upwelling and the absence of El Niño) in the northern area and between January and October during the event El Niño 2006, in the southern area (with seasonal upwelling). In this study we determined in total 23 species, 22 which were collected off Iquique and 16 off Concepción. Furthermore, we determined the following parameters: carbonate and individual fluxes and the diversity in order to define faunal patterns in these areas in different oceanographic conditions. The results show that off Iquique (20°S) under normal conditions, there is a constant individual and carbonate flux, with peaks in September and October 2005 reaffirming the presence of coastal upwelling in this period. In contrast, off Concepción, under El Niño 2006, the individuals and calcium carbonate fluxes exhibits maxima during the summer upwelling showing however are of shorter duration (January-February) compared to that described in normal conditions for this area. The diversity was higher to a lower depth in the both areas remained constant throughout the period in the northern area, in contrast to the southern area, whose highest values were observed during the summer coinciding with coastal upwelling in this area.